export(

SPIA, DEGraph, Clipper, PRS, PWEA, TAPPA, TopologyGSA,
res, topo.sig, degtable,
AdjacencyMatrix2pathway,
graphNEL2pathway,
estimateCF,
reduceGraph,
convertIdentifiersByVector,
KEGG2pathway,
makeDefaultEdgeData,
prepareTIF, collectWeightsPRS, collectWeightsSPIA,
preparePathways
)

useDynLib(ToPASeq)

exportClasses(pathway)
exportMethods(nodes, edges)
exportMethods(intersection, join, union, subGraph, clearNode, removeEdge, removeNode, addEdge, addNode, changeDirection, changeInteraction,"nodes<-")

exportMethods(degree, numNoEdges, mostEdges, acc, connComp, edges, isAdjacent, isDirected, isConnected, edgemode, numEdges, numNodes, edgeNames)


S3method(print, topResult)
S3method(topo.sig, topResult)
S3method(degtable, topResult)
S3method(res, topResult)
S3method(summary, topResult)
S3method(plot,topResult)

import(graphite, gRbase, graph, locfit, methods, Rgraphviz)
importFrom(DESeq2, DESeqDataSetFromMatrix, DESeq, results, estimateSizeFactors, estimateDispersions, nbinomWaldTest, rlogTransformation, varianceStabilizingTransformation)
importFrom(GenomicRanges, assay, colData, "colData<-")
importFrom(KEGGgraph, parseKGML)

importFrom(R.utils, reassignInPackage)
importFrom(edgeR,DGEList, calcNormFactors)

importFrom(parallel, detectCores, makeCluster, clusterExport, parSapply, stopCluster)
importClassesFrom(Biobase, ExpressionSet)
importMethodsFrom(Biobase, exprs, pData)

importFrom(DESeq, newCountDataSet, estimateSizeFactors, estimateDispersions)
importFrom(fields, image.plot)
importFrom(TeachingDemos, shadowtext)
importFrom(limma,  lmFit, makeContrasts, contrasts.fit, eBayes, decideTests, topTable, voom) 
importMethodsFrom(graph, edgeData, edgeDataDefaults)


importFrom(qpgraph,qpIPF)
importFrom(RBGL,johnson.all.pairs.sp)
importFrom(clipper, easyClip, pathQ, cliqueMeanTest, cliqueVarianceTest)